Can anyone direct me to a quick guide/list of Tokyo subway/train stops close to popular attractions? Im having trouble finding information that lists the particular stations so I can plan out our daily route. I know Tokyo is a huge city, but it is diffucult to tell from my maps how far different attractions are away from the stations., or which station to use. Are there info boards inside the stations that list what exit to use for a major attraction? I cant see how I can successfully use Hyperdia unless I know what particular station that I need.

Basically just about all the stations are near something. You need to pin down what exactly a "popular attraction" is - and everyone has their own idea of what "far" is too. In my last time going through Tokyo I typically walked 8-12 miles a day. You may or may not be eager to do the same. I suggest you forget about what is "popular", and concentrate on what you like - popular or not.
If you look at a site like Japan Guide, you will find lots of Tokyo places listed, as well as access info on how to get there. Have you used Google Maps? You can see quite clearly what station is near someplace for you and how much walking it takes to get the rest of the way. It shows its scale, so you can easily guesstimate how many feet or meters away a place is. And in general a person walks about 3 mph or 5 kph. Many attraction websites list access info too.

For your other question, yes, most Japanese stations have multiple exits and clearly list what major places (tourist places and others) are close by. But it certainly would help if you look up places before your departure and at least find which direction to take - even just "north exit", "south exit" etc.
It seems to me you may be putting the cart before the horse here. You might try the reverse - find the places you want to see first, then find the best way to get there.

I have found with google maps that if you zoom carefully you can see the station exit number....very helpful....

.... and Apple maps. Almost all subway/train stations will have a list of exits, listing the local "popular attractions" (though they may be listed by exit, rather than by attraction name, so you may need to scan the list of exits to find the attraction you want). Also, most stations will have a large-scale map of the local area so, if your attraction is not listed, check that to figure out the most appropriate exit.

It's really not that difficult to figure out which subway/train station is closest to any particular 'attraction' - just study the map. Depending on what guidebook you're using, as often as not it will tell you what station/exit is closest or look at the website etc. for the attraction (if there is one).

I don't know if you will have a Japan Rail Pass (probably not if you're only visiting Tokyo)? If so, it may be tempting to use the JR Yamanote line (a 30-station, 60 minute loop around Tokyo) on the basis that it's free with the Pass - but it may not be the fastest way of getting where you're going. Other JR train lines (e.g., the JR Chuo line) may be quicker, as may the subway - get the Tokyo Metro app on your phone. Note that the app has a 'search by landmark' function which (If your landmark is listed) will tell you the nearest subway station. However, be aware that taking the subway from wherever you happen to be to that station may not be the quickest way of getting there, depending on which lines you need to take and where they connect.

Get a Suica card - a prepaid travel card. Much, much easier to use than having to stop to get a ticket every time you want to get on the subway or a train.

IME, many web-sites for places had clear information about which stations, with what exits, and what distance / directions from the exits.

I found that far easier than the lists of places near exits within many station -- some stations have so many exits, with so many nearby locations, they I found it hard to use the information, particularly if the station was busy. JMO.